[gmx-users] Fatal error:No molecules were defined in the system

[Justin Lemkul]

On 10/20/14 11:19 AM, Nilesh Dhumal wrote:
> Hello,
>
> For grompp
>
> grompp -f minim_hy.mdp -c cu.gro -p test.top -o 1.tpr
>
> I get the error" Fatal error:No molecules were defined in the system"
>
> Here I pasted initial part of test.top file.
>
>
>
>
> ; Derived from parsing of runfiles/alat.top.orig
> [ defaults ]
> ; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
>   1               3               yes             0.5     0.5
> ; comb-rule 3 is square-root sigma, the OPLSAA version
>
> [ atomtypes ]
> ; full atom descriptions are available in ffoplsaa.atp
> ; name  bond_type    mass    charge   ptype          sigma      epsilon
>   opls_991   Cu    29	63.54600    1.098       A    3.114e-01    0.02092e+00
>   opls_993   OA    8     15.99940    -0.665       A    3.033e-01
> 0.401664e+00
>   opls_994   OB    8     15.99940    -0.665       A    3.033e-01
> 0.401664e+00
>   opls_995   CA    6     12.0110      0.778       A    3.473e-01
> 0.39748e+00
>   opls_996   CB    6     12.0110     -0.092       A    3.473e-01
> 0.39748e+00
>   opls_997   CC    6     12.0110     -0.014       A    3.473e-01
> 0.39748e+00
>   opls_998   HM    1      1.0080      0.109       A    2.846e-01
> 0.06276e+00
>
> [ moleculetype ]
> ; Name            nrexcl
>   BTC             3
>
> [ atoms ]
> ;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB
>     chargeB      massB
>    1    opls_993      1    BTC    OA       1    -0.665    15.99940
>    2    opls_995      1    BTC    CA       2     0.778    12.01100
>    3    opls_996      1    BTC    CB       3    -0.092    12.01100
>    4    opls_997      1    BTC    CC       4    -0.014    12.01100
>    5    opls_998      1    BTC    HM       5     0.109     1.00800
>    6    opls_997      1    BTC    CC       6    -0.014    12.01100
>    7    opls_998      1    BTC    HM       7     0.109     1.00800
>    8    opls_993      1    BTC    OA       8    -0.665    15.99940
>    9    opls_995      1    BTC    CA       9     0.778    12.01100
>   10    opls_996      1    BTC    CB      10    -0.092    12.01100
>   11    opls_997      1    BTC    CC      11    -0.014    12.01100
>   12    opls_998      1    BTC    HM      12     0.109     1.00800
>   13    opls_993      1    BTC    OA      13    -0.665    15.99940
>   14    opls_995      1    BTC    CA      14     0.778    12.01100
>   15    opls_996      1    BTC    CB      15    -0.092    12.01100
>   16    opls_994      1    BTC    OB      16    -0.665    15.99940
>   17    opls_994      1    BTC    OB      17    -0.665    15.99940
>   18    opls_994      1    BTC    OB      18    -0.665    15.99940
>   19    opls_993      1    BTC    OA      19    -0.665    15.99940
>   20    opls_995      1    BTC    CA      20     0.778    12.01100
>
> Is there any error in .top file?
>

There is no way to tell unless you provide the full file.  Either there is a 
syntax error somewhere that breaks the parsing, or your [molecules] section is 
empty.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================